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Wu B, Lan X, Gao M, Wei W, Wang Y, Yang Y, Yu Z, Huang M, Wu Q. Elucidation of the molecular mechanism of type 2 diabetes mellitus affecting the progression of nonalcoholic steatohepatitis using bioinformatics and network pharmacology: A review. Medicine (Baltimore) 2024; 103:e39731. [PMID: 39287256 PMCID: PMC11404948 DOI: 10.1097/md.0000000000039731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/19/2024] Open
Abstract
Increasing evidence suggests that patients with diabetes are at increased risk of developing nonalcoholic steatohepatitis (NASH), but the underlying mechanisms that affect the progression of NASH remain unclear. In this study, we used bioinformatics and network pharmacology methods to explore the differentially expressed genes of NASH and the related genes of type 2 diabetes mellitus, and a total of 46 common targets were obtained. Gene ontology showed that the common targets were mainly involved in biological processes such as glucocorticoid, hormone, and bacterium responses. The Kyoto Encyclopedia of Genes and Genomes enrichment analysis signal pathways were mainly in colorectal cancer, amphetamine addition, the peroxisome proliferator-activated receptor signaling pathway, and the toll-like receptor signaling pathway. The protein-protein interaction network identified 8 hub genes, and the co-expression network was analyzed to obtain 7 related functions and mutual proportions of hub genes. A total of 120 transcription factors were predicted for hub genes. Hub genes were closely related to immune cells, including neutropils and eosinophils. In addition, we identified 15 potential candidate drugs based on hub genes that are promising for the treatment of NASH. Type 2 diabetes mellitus can affect the progression of NASH by changing hormone levels and inflammatory responses through multiple targets and signaling pathways. Eight hub genes are expected to be potential targets for subsequent treatment.
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Affiliation(s)
- Bo Wu
- Department of Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Xiaohong Lan
- Department of Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Ming Gao
- Department of Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Wei Wei
- Department of Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Yuekun Wang
- Department of Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Yang Yang
- Department of Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Zhiyang Yu
- The fourth was assigned to the outpatient department, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Min Huang
- Department of Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Qinyan Wu
- Department of Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
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Kong FX, Liu H, Xu T, Li SJ, Li W, Lu H, Ma NN, Wang YL, Shi JH, Yang YR, Wang FL. RG108 attenuates acute kidney injury by inhibiting P38 MAPK/FOS and JNK/JUN pathways. Int Immunopharmacol 2024; 142:113077. [PMID: 39265353 DOI: 10.1016/j.intimp.2024.113077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 08/16/2024] [Accepted: 09/01/2024] [Indexed: 09/14/2024]
Abstract
Acute kidney injury (AKI) is an important clinical syndrome characterised by a sudden decline in renal function, often accompanied by renal inflammation and tubular epithelial cell damage. It has been reported that inhibiting DNA methylation significantly suppress the progression of AKI. In the current study, we investigate the effect of the DNA methyltransferase (DNMT) inhibitor RG108 in cisplatin- and hypoxia-reoxygenation-induced AKI. The expression of kidney injury molecules and inflammatory factors was examined by immunofluorescence, Western blotting and Real-time PCR. The results demonstrated that RG108 treatment significantly reduced kidney inflammation and injury. Furthermore, RNA-seq analysis was performed to reveal the regulatory mechanism of RG108 in AKI. The expression of the FOS and JUN genes, which are downstream of the MAPK pathway, were significant increased in AKI. Meanwhile, the expression of FOS and JUN were both inhibited by RG108, which is similar to what we found treatment with a specific JNK inhibitor and a specific p38 MAPK inhibitor, and thus attenuated renal inflammation and injury. In conclusion, we suggest that RG108 inhibits P38 MAPK/FOS and JNK/JUN pathways and attenuates renal injury and inflammatory responses. In these results, RG108 may become a novel MAPK pathway inhibitor and a clinical candidate for the treatment of AKI.
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Affiliation(s)
- Fan-Xu Kong
- School of Pharmacy, Anhui Medical University, Hefei 230032, China; The Second People's Hospital of Hefei, Hefei 230011, Anhui, China
| | - Hui Liu
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, China
| | - Tao Xu
- School of Pharmacy, Anhui Medical University, Hefei 230032, China; The Second People's Hospital of Hefei, Hefei 230011, Anhui, China
| | - Shuang-Jian Li
- School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Wei Li
- School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Hao Lu
- School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Nan-Nan Ma
- Jiangsu Huaiyin Maternity and Children's Hospital, Jiangsu 223399, China
| | - Yun-Long Wang
- School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Ji-Hong Shi
- Jiangsu Huaiyin Maternity and Children's Hospital, Jiangsu 223399, China
| | - Ya-Ru Yang
- School of Pharmacy, Anhui Medical University, Hefei 230032, China.
| | - Feng-Ling Wang
- School of Pharmacy, Anhui Medical University, Hefei 230032, China; The Second People's Hospital of Hefei, Hefei 230011, Anhui, China.
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Smith JP, Paxton R, Medrano S, Sheffield NC, Sequeira-Lopez MLS, Ariel Gomez R. Inhibition of Renin Expression Is Regulated by an Epigenetic Switch From an Active to a Poised State. Hypertension 2024; 81:1869-1882. [PMID: 38989586 PMCID: PMC11337216 DOI: 10.1161/hypertensionaha.124.22886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024]
Abstract
BACKGROUND Renin-expressing cells are myoendocrine cells crucial for the maintenance of homeostasis. Renin is regulated by cAMP, p300 (histone acetyltransferase p300)/CBP (CREB-binding protein), and Brd4 (bromodomain-containing protein 4) proteins and associated pathways. However, the specific regulatory changes that occur following inhibition of these pathways are not clear. METHODS We treated As4.1 cells (tumoral cells derived from mouse juxtaglomerular cells that constitutively express renin) with 3 inhibitors that target different factors required for renin transcription: H-89-dihydrochloride, PKA (protein kinase A) inhibitor; JQ1, Brd4 bromodomain inhibitor; and A-485, p300/CBP inhibitor. We performed assay for transposase-accessible chromatin with sequencing (ATAC-seq), single-cell RNA sequencing, cleavage under targets and tagmentation (CUT&Tag), and chromatin immunoprecipitation sequencing for H3K27ac (acetylation of lysine 27 of the histone H3 protein) and p300 binding on biological replicates of treated and control As4.1 cells. RESULTS In response to each inhibitor, Ren1 expression was significantly reduced and reversible upon washout. Chromatin accessibility at the Ren1 locus did not markedly change but was globally reduced at distal elements. Inhibition of PKA led to significant reductions in H3K27ac and p300 binding specifically within the Ren1 super-enhancer region. Further, we identified enriched TF (transcription factor) motifs shared across each inhibitory treatment. Finally, we identified a set of 9 genes with putative roles across each of the 3 renin regulatory pathways and observed that each displayed differentially accessible chromatin, gene expression, H3K27ac, and p300 binding at their respective loci. CONCLUSIONS Inhibition of renin expression in cells that constitutively synthesize and release renin is regulated by an epigenetic switch from an active to poised state associated with decreased cell-cell communication and an epithelial-mesenchymal transition. This work highlights and helps define the factors necessary for renin cells to alternate between myoendocrine and contractile phenotypes.
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Affiliation(s)
- Jason P. Smith
- Department of Pediatrics, Child Health Research Center, University of Virginia, Charlottesville, Virginia
| | - Robert Paxton
- Department of Pediatrics, Child Health Research Center, University of Virginia, Charlottesville, Virginia
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Silvia Medrano
- Department of Pediatrics, Child Health Research Center, University of Virginia, Charlottesville, Virginia
| | - Nathan C. Sheffield
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia
| | | | - R. Ariel Gomez
- Department of Pediatrics, Child Health Research Center, University of Virginia, Charlottesville, Virginia
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Liu X, Zhang X, Yao C, Liang J, Noble PW, Jiang D. Transcriptomics Analysis Identifies the Decline in the Alveolar Type II Stem Cell Niche in Aged Human Lungs. Am J Respir Cell Mol Biol 2024; 71:229-241. [PMID: 38635761 PMCID: PMC11299088 DOI: 10.1165/rcmb.2023-0363oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 04/18/2024] [Indexed: 04/20/2024] Open
Abstract
Aging poses a global public health challenge, which is linked to the rise of age-related lung diseases. The precise understanding of the molecular and genetic changes in the aging lung that elevate the risk of acute and chronic lung diseases remains incomplete. Alveolar type II (AT2) cells are stem cells that maintain epithelial homeostasis and repair the lung after injury. AT2 progenitor function decreases with aging. The maintenance of AT2 function requires niche support from other cell types, but little has been done to characterize alveolar alterations with aging in the AT2 niche. To systematically profile the genetic changes associated with age, we present a single-cell transcriptional atlas comprising nearly half a million cells from the healthy lungs of human subjects spanning various ages, sexes, and smoking statuses. Most annotated cell lineages in aged lungs exhibit dysregulated genetic programs. Specifically, the aged AT2 cells demonstrate loss of epithelial identities, heightened inflammaging characterized by increased expression of AP-1 (Activator Protein-1) transcription factor and chemokine genes, and significantly increased cellular senescence. Furthermore, the aged mesenchymal cells display a remarkable decrease in collagen and elastin transcription and a loss of support to epithelial cell stemness. The decline of the AT2 niche is further exacerbated by a dysregulated genetic program in macrophages and dysregulated communications between AT2 and macrophages in aged human lungs. These findings highlight the dysregulations observed in both AT2 stem cells and their supportive niche cells, potentially contributing to the increased susceptibility of aged populations to lung diseases.
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Affiliation(s)
- Xue Liu
- Department of Medicine and Women’s Guild Lung Institute and
| | - Xuexi Zhang
- Department of Medicine and Women’s Guild Lung Institute and
| | - Changfu Yao
- Department of Medicine and Women’s Guild Lung Institute and
| | - Jiurong Liang
- Department of Medicine and Women’s Guild Lung Institute and
| | - Paul W. Noble
- Department of Medicine and Women’s Guild Lung Institute and
| | - Dianhua Jiang
- Department of Medicine and Women’s Guild Lung Institute and
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
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Wrońska A, Kieżun J, Kmieć Z. High-Dose Fenofibrate Stimulates Multiple Cellular Stress Pathways in the Kidney of Old Rats. Int J Mol Sci 2024; 25:3038. [PMID: 38474282 DOI: 10.3390/ijms25053038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
We investigated the age-related effects of the lipid-lowering drug fenofibrate on renal stress-associated effectors. Young and old rats were fed standard chow with 0.1% or 0.5% fenofibrate. The kidney cortex tissue structure showed typical aging-related changes. In old rats, 0.1% fenofibrate reduced the thickening of basement membranes, but 0.5% fenofibrate exacerbated interstitial fibrosis. The PCR array for stress and toxicity-related targets showed that 0.1% fenofibrate mildly downregulated, whereas 0.5% upregulated multiple genes. In young rats, 0.1% fenofibrate increased some antioxidant genes' expression and decreased the immunoreactivity of oxidative stress marker 4-HNE. However, the activation of cellular antioxidant defenses was impaired in old rats. Fenofibrate modulated the expression of factors involved in hypoxia and osmotic stress signaling similarly in both age groups. Inflammatory response genes were variably modulated in the young rats, whereas old animals presented elevated expression of proinflammatory genes and TNFα immunoreactivity after 0.5% fenofibrate. In old rats, 0.1% fenofibrate more prominently than in young animals induced phospho-AMPK and PGC1α levels, and upregulated fatty acid oxidation genes. Our results show divergent effects of fenofibrate in young and old rat kidneys. The activation of multiple stress-associated effectors by high-dose fenofibrate in the aged kidney warrants caution when applying fenofibrate therapy to the elderly.
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Affiliation(s)
- Agata Wrońska
- Department of Histology, Faculty of Medicine, Medical University of Gdańsk, 80-210 Gdańsk, Poland
| | - Jacek Kieżun
- Department of Human Histology and Embryology, School of Medicine, University of Warmia and Mazury in Olsztyn, 10-082 Olsztyn, Poland
| | - Zbigniew Kmieć
- Department of Histology, Faculty of Medicine, Medical University of Gdańsk, 80-210 Gdańsk, Poland
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Jo MJ, Lee JK, Kim JE, Ko GJ. Molecular Mechanisms Associated with Aging Kidneys and Future Perspectives. Int J Mol Sci 2023; 24:16912. [PMID: 38069234 PMCID: PMC10707287 DOI: 10.3390/ijms242316912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
The rapid growth of the elderly population is making the need for extensive and advanced information about age-related organ dysfunction a crucial research area. The kidney is one of the organs most affected by aging. Aged kidneys undergo functional decline, characterized by a reduction in kidney size, decreased glomerular filtration rate, alterations in renal blood flow, and increased inflammation and fibrosis. This review offers a foundation for understanding the functional and molecular mechanisms of aging kidneys and for selecting identifying appropriate targets for future treatments of age-related kidney issues.
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Affiliation(s)
- Min-Jee Jo
- Department of Internal Medicine, Korea University College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea; (M.-J.J.); (J.-K.L.); (J.-E.K.)
- Institute of Convergence New Drug Development, Korea University College of Medicine, Seoul 08308, Republic of Korea
| | - Joo-Kyung Lee
- Department of Internal Medicine, Korea University College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea; (M.-J.J.); (J.-K.L.); (J.-E.K.)
| | - Ji-Eun Kim
- Department of Internal Medicine, Korea University College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea; (M.-J.J.); (J.-K.L.); (J.-E.K.)
| | - Gang-Jee Ko
- Department of Internal Medicine, Korea University College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea; (M.-J.J.); (J.-K.L.); (J.-E.K.)
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Lissek T. Aging, adaptation and maladaptation. FRONTIERS IN AGING 2023; 4:1256844. [PMID: 37701757 PMCID: PMC10493302 DOI: 10.3389/fragi.2023.1256844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023]
Abstract
Aging is accompanied by a dysregulation of adaptive processes. On the one hand, physiological adaptation mechanisms such as learning and memory, immune system plasticity and exercise-dependent muscle remodeling are blunted. On the other hand, several maladaptive processes increase with age including cancer, pathological cardiovascular remodeling and metabolic dysregulation. With increasing age the quotient of beneficial adaptation (Ab) to harmful adaptation (Ah), Ab/Ah, decreases. The adaptation-maladaptation framework of aging entails that there are age-related pathological phenotypes that are the result of activation of physiological adaptation mechanisms (e.g., maladaptation as a result of misdirection of adaptive cascades and molecular damage incurred by adaptation processes) and their occurrence over time might, to some degree, be inevitable. Aging might hence result from the organism's inability to solve the adaptation-maladaptation dilemma. The present work explores the concept of counteracting aging through adaptation and proposes that interventions such as exercise, environmental enrichment and dietary restriction work in counteracting aging because they increase the ratio Ab/Ah by both raising Ab (e.g., by inducing metaplasticity in cells, meaning they raise the adaptability of cells to future stimuli) and decreasing Ah (e.g., through desensitizing certain potentially harmful adaptive mechanisms). Molecules whose aging-related expression changes can explain aspects of dysfunctional adaptation such as CREB and certain immediate early genes are examined and it is delineated how a better understanding of the dynamical organization of adaptation cascades could elucidate the seemingly complex role of adaptation in driving aging as well as protecting against it.
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Affiliation(s)
- Thomas Lissek
- Interdisciplinary Center for Neurosciences, Heidelberg University, Heidelberg, Germany
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